Create biobambam markduplicates 2 cram step

modules/VRPipe/Steps/biobambam_mark_duplicates_two.pm

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+
+=head1 NAME
+
+VRPipe::Steps::biobambam_mark_duplicates_two - a step
+
+=head1 DESCRIPTION
+
+Runs the biobambam's mark duplicates 2 to mark duplicates.
+
+=head1 AUTHOR
+
+Martin Pollard <[email protected]>.
+
+=head1 COPYRIGHT AND LICENSE
+
+Copyright (c) 2015 Genome Research Limited.
+
+This file is part of VRPipe.
+
+VRPipe is free software: you can redistribute it and/or modify it under the
+terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+PARTICULAR PURPOSE. See the GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along with
+this program. If not, see L<http://www.gnu.org/licenses/>.
+
+=cut
+
+use VRPipe::Base;
+
+class VRPipe::Steps::biobambam_mark_duplicates_two with VRPipe::StepRole {
+
+    method options_definition {
+        return {
+            bammarkduplicates2_exe     => VRPipe::StepOption->create(description => 'path to bammarkduplicates2 executable', optional => 1, default_value => 'bammarkduplicates2'),
+            bammarkduplicates2_opts    => VRPipe::StepOption->create(description => 'bammarkduplicates2 options (excluding arguments that set input/output file names and threads)', optional => 1, default_value => ''),
+            bammarkduplicates2_threads => VRPipe::StepOption->create(description => 'number of threads to use', optional => 1, default_value => '1'),
+            tmp_dir                    => VRPipe::StepOption->create(description => 'location for tmp directories; defaults to working directory', optional => 1),
+        };
+    }
+
+    method inputs_definition {
+        return {
+            cram_files => VRPipe::StepIODefinition->create(
+                type        => 'cram',
+                max_files   => -1,
+                description => '1 or more coordinate sorted CRAM files',
+                metadata    => {
+                    lane             => 'lane name (a unique identifer for this sequencing run, aka read group)',
+                    bases            => 'total number of base pairs',
+                    reads            => 'total number of reads (sequences)',
+                    forward_reads    => 'number of forward reads',
+                    reverse_reads    => 'number of reverse reads',
+                    paired           => '0=single ended reads only; 1=paired end reads present',
+                    mean_insert_size => 'mean insert size (0 if unpaired)',
+                    avg_read_length  => 'the average length of reads',
+                    library          => 'library name',
+                    sample           => 'sample name',
+                    center_name      => 'center name',
+                    platform         => 'sequencing platform, eg. ILLUMINA|LS454|ABI_SOLID',
+                    study            => 'name of the study, put in the DS field of the RG header line',
+                    optional         => ['lane', 'library', 'sample', 'center_name', 'platform', 'study', 'mean_insert_size', 'forward_reads', 'reverse_reads', 'paired', 'avg_read_length']
+                }
+            ),
+        };
+    }
+
+    method body_sub {
+        return sub {
+            my $self            = shift;
+            my $options         = $self->options;
+            my $bammarkduplicates2_exe     = $options->{bammarkduplicates2_exe};
+            my $bammarkduplicates2_opts    = $options->{bammarkduplicates2_opts};
+            my $bammarkduplicates2_threads = $options->{bammarkduplicates2_threads};
+
+            $self->set_cmd_summary(
+                VRPipe::StepCmdSummary->create(
+                    exe     => 'bammarkduplicates2',
+                    version => VRPipe::StepCmdSummary->determine_version($bammarkduplicates2_exe . ' --version', '^This is biobambam version (.+)\.$'),
+                    summary => "bammarkduplicates2 $bammarkduplicates2_opts I:\$bam_file O:\$output_file(s)"
+                )
+            );
+
+            my $req = $self->new_requirements(memory => 3000, time => 1, cpus => $bammarkduplicates2_threads);
+
+            my $input_files = join ' ', (map {$_ = "I=".$_->path;} (@{ $self->inputs->{cram_files} }));
+            my $merged_metadata = $self->common_metadata($self->inputs->{cram_files});
+            my $basename = $self->stepstate->dataelement->id . '.cram';
+            my $markdup_bam_file = $self->output_file(
+                output_key => 'markdup_cram_files',
+                basename   => 'mark_merge',
+                type       => 'cram',
+                metadata   => $merged_metadata
+            );
+            my $tmpdir = $options->{tmp_dir} || $markdup_bam_file->dir;
+            my $threads = "";
+            $threads = " markthreads=$bammarkduplicates2_threads" if $bammarkduplicates2_threads ne '1';
+            my $this_cmd = "$bammarkduplicates2_exe ${bammarkduplicates2_opts}${threads} tmpfile=$tmpdir $input_files O=" . $markdup_bam_file->path . " $bammarkduplicates2_opts";
+
+            $self->dispatch_wrapped_cmd('VRPipe::Steps::biobambam_mark_duplicates_two', 'markdup_and_check', [$this_cmd, $req, { output_files => [$markdup_bam_file] }]);
+        };
+    }
+
+    method outputs_definition {
+        return {
+            markdup_cram_files => VRPipe::StepIODefinition->create(type => 'cram', max_files => 1, description => 'a cram file with duplicates marked'),
+        };
+    }
+
+    method post_process_sub {
+        return sub { return 1; };
+    }
+
+    method description {
+        return "Marks duplicates in CRAM files using biobambam";
+    }
+
+    method max_simultaneous {
+        return 0;          # meaning unlimited
+    }
+
+    method markdup_and_check (ClassName|Object $self: Str $cmd_line) {
+        my ($out_path) = $cmd_line =~ /O=(\S+)/;
+        $out_path || $self->throw("cmd_line [$cmd_line] was not constructed as expected");
+        my @inputs = $cmd_line =~ /I=(\S+)/g;
+        (scalar @inputs)  || $self->throw("cmd_line [$cmd_line] was not constructed as expected");
+        my $expected_reads = 0;
+        foreach my $in_path (@inputs) {
+            my $in_file  = VRPipe::File->get(path => $in_path);
+            $in_file->disconnect;
+            $expected_reads += $in_file->metadata->{reads} || $in_file->num_records;
+        }
+        my $out_file = VRPipe::File->get(path => $out_path);
+
+        system($cmd_line) && $self->throw("failed to run [$cmd_line]");
+
+        $out_file->update_stats_from_disc(retries => 3);
+        my $actual_reads = $out_file->num_records;
+
+        if ($actual_reads == $expected_reads) {
+            return 1;
+        }
+        else {
+            $out_file->unlink;
+            $self->throw("cmd [$cmd_line] failed because $actual_reads reads were generated in the output CRAM file, yet there were $expected_reads reads in the original CRAM file");
+        }
+    }
+}
+
+1;

t/VRPipe/Steps/biobambam_mark_duplicates_two.t

@@ -0,0 +1,35 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Path::Class;
+use POSIX qw(getgroups);
+
+BEGIN {
+    use Test::Most tests => 2;
+    use VRPipeTest (required_env => [qw(VRPIPE_TEST_PIPELINES)]);
+    use TestPipelines;
+
+    use_ok('VRPipe::Steps::biobambam_mark_duplicates_two');
+}
+
+my ($output_dir, $pipeline, $step) = create_single_step_pipeline('biobambam_mark_duplicates_two', 'cram_files');
+is_deeply [$step->id, $step->description], [1, 'Marks duplicates in CRAM files using biobambam'], 'biobambam_mark_duplicates_two step created and has correct description';
+
+my $setup = VRPipe::PipelineSetup->create(
+    name       => 'biobambam_mark_duplicates_two',
+    datasource => VRPipe::DataSource->create(
+        type    => 'fofn_with_metadata',
+        method  => 'grouped_by_metadata',
+        source  => file(qw(t data cram.fofn_with_metadata))->absolute->stringify,
+        options => {
+            metadata_keys = 'sample',
+        }
+    },
+    output_root => $output_dir,
+    pipeline    => $pipeline,
+    options     => {}
+};
+
+ok handle_pipeline(), 'biobambam_mark_duplicates_two pipeline ran ok';
+
+finish;

t/data/cram.fofn_with_metadata

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+path	lane	paired	reads	bases